rs2682562

chr19-43536845-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.163 in 152,168 control chromosomes in the GnomAD database, including 2,092 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24746 AN: 152050 Hom.: 2094 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.155

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.163 AC: 24758 AN: 152168 Hom.: 2092 Cov.: 32 AF XY: 0.160 AC XY: 11920 AN XY: 74382

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.153

Alfa AF: 0.180 Hom.: 861

Bravo AF: 0.157

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.6
Dann	Benign	0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2682562; hg19: chr19-44040997;